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# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
from Numeric import *
from VQT import *
from string import *
import re
keypat = re.compile("(\S+)")
molpat = re.compile("mol \(.*\) (\S\S\S)")
atompat = re.compile("atom (\d+) \((\d+)\) \((-?\d+), (-?\d+), (-?\d+)\)")
def readmmp(fname):
pos = []
elt = []
atnum = -1
atnos = {}
bonds = []
for card in open(fname).readlines():
key = keypat.match(card).group(1)
if key == 'atom':
atnum += 1
m = atompat.match(card)
atnos[int(m.group(1))] = atnum
elt += [int(m.group(2))]
pos += [map(float, [m.group(3),m.group(4),m.group(5)])]
if key[:4] == 'bond':
order = ['1','2','3','a','g'].index(key[4])
bonds += [(atnum,atnos[int(x)],order)
for x in re.findall("\d+",card[5:])]
pos = array(pos)/1000.0
return elt, pos, array(bonds)
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